If you are using Firefox, then the noscript add-on is an option. Most of these ads are loaded by script and Noscript will block that. Though this will leave you with sites that depend on script for their basic purpose not working in other ways.
Another option (again Firefox only, though there are no doubt ways to do the same in other recent browsers) is aardvark which lets you manually remove the floaters. I find this handy for removing excess content when printing pages too. This is a manual process, but less of a blunt instrument than noscript. There are some places that are getting wise to such DOM manipulation though, specifically those hawking Microsoft's Silverlight - those floaters seem to detect that you have removed when and they replace themselves (as I've never come across anything on such an affected site that I can't get from many others I just add these sites to my "will never visit again" list, enforced by hosts file entry, and move on).
What you are looking for really is something that automatically does what can be done with aardvark without disabling all script. Unfortunately this is a significant problem as there are many ways to arrange floaters so such a tool would have to carry configuration for each site and would need to support a number of methods of removal, so would be much more of a chore to develop and maintain than noscript and aardvark. Writing something (an add-on or some sort of proxy based filter) to automatically detect and deal with floaters would require a level of AI not currently available (or, at least not currently remotely close to being practical to implement for this purpose!) as there are many ways to implement them and all could be mistake for more useful UI elements so false positives would be a noticeable problem.
Update:
Some years later, things have moved on... In modern browsers you don't need add-ons like Aarvark: the built in debugging tools allow you to monkey around with the DOM to remove parts you don't want. In Chrome, Firefoz, and modern ID, right-click and pick "inspect element" to be taken to the DOM explorer form where you can delete or edit elements to your hearts content. I sometimes use this to create printable versions of pages that "reading view" modes don't work well on for that (I don't use it much for irritating pop-overs - when they appear I tend to just close that tab and move on). If you are wary of right-clicking being taken as an action, open the debugging tools by pressing F12 and navigate to the right part of the DOM explorer that way.
Of course this is all very manual and requires some knowledge of HTML, particularly for some complex pages where knowing what to delete/edit and what not can be unclear, so for ad-blocking automated add-ins specific to that and/or the likes of noscript (or just leaving sites that irritate you in that way and never coming back!) are the way to go.
1This particular site in the bounty can not do what it does without javascript actions. disabling javascript completly worked, with firefox "noscript" should be capable of it, in IE advanced options can disable that, but it is not convienient to turn back on. Without avoiding sites like this altogether we do end up feeding the trolls, they will never learn and never change. – Psycogeek – 2014-10-06T10:35:54.073
Can you give an examle page, where they have su ch adds you refer to? – rubo77 – 2014-10-10T23:27:03.637
1A lot of these ads offer the option to disable themselves. When you hover over a word and the ad appears llok and see if there's a question mark, or a link to settings. – alex – 2009-10-28T09:31:58.413
Put that in an answer, dude, so I can give you creds for it. I have never noticed this and it is great! – wzzrd – 2009-10-28T09:44:41.023
1Call be paranoid, by I'm wary of clicking anywhere in a floating ad, at lease those on non "big name" sites. How do you know without reviewing the code that clicking the question mark or any other hot-spot won't instead open a series of pop-up/under windows or some such... Hence I used the aardvark option to remove the content while interacting with it as little as possible. – David Spillett – 2009-10-28T13:25:42.467